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  "Title": "Maximum Likelihood Analysis of Animal Movement Behavior Using\nMultivariate Hidden Markov Models",
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  "Date": "2025-11-24",
  "Authors@R": "c(person(given = \"Brett\",\nfamily = \"McClintock\",\nrole = c(\"aut\", \"cre\"),\nemail = \"brett.mcclintock@noaa.gov\"),\nperson(given = \"Theo\",\nfamily = \"Michelot\",\nrole = \"aut\"))",
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  "Date/Publication": "2025-11-25 00:41:41 UTC",
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    "plotPR",
    "plotSat",
    "plotSpatialCov",
    "plotStates",
    "plotStationary",
    "prepData",
    "pseudoRes",
    "randomEffects",
    "setModelName",
    "setStateNames",
    "simData",
    "simHierData",
    "simObsData",
    "stateProbs",
    "stationary",
    "timeInStates",
    "viterbi"
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      "title": "Example dataset",
      "object": "example",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "forest",
      "title": "Example dataset",
      "object": "forest",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "miExample",
      "title": "Example dataset",
      "object": "miExample",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
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      "topics": [
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      ]
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      "title": "Calculate Akaike information criterion model weights",
      "topics": [
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      ]
    },
    {
      "page": "allProbs",
      "title": "Matrix of all probabilities",
      "topics": [
        "allProbs"
      ]
    },
    {
      "page": "checkPar0",
      "title": "Check parameter length and order for a 'fitHMM' (or 'MIfitHMM') model",
      "topics": [
        "checkPar0",
        "checkPar0.default",
        "checkPar0.hierarchical"
      ]
    },
    {
      "page": "CIbeta",
      "title": "Confidence intervals for working (i.e., beta) parameters",
      "topics": [
        "CIbeta"
      ]
    },
    {
      "page": "circAngles",
      "title": "Convert standard direction angles (in radians relative to the x-axis) to turning angle covariates suitable for circular-circular regression on the angle mean",
      "topics": [
        "circAngles"
      ]
    },
    {
      "page": "CIreal",
      "title": "Confidence intervals for the natural (i.e., real) parameters",
      "topics": [
        "CIreal",
        "CIreal.default",
        "CIreal.hierarchical"
      ]
    },
    {
      "page": "crawlMerge",
      "title": "Merge crwData or crwHierData object with additional data streams and/or covariates",
      "topics": [
        "crawlMerge"
      ]
    },
    {
      "page": "crawlWrap",
      "title": "Fit and predict tracks for using crawl",
      "topics": [
        "crawlWrap"
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    },
    {
      "page": "crwData",
      "title": "Constructor of 'crwData' objects",
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        "crwData"
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    {
      "page": "crwHierData",
      "title": "Constructor of 'crwHierData' objects",
      "topics": [
        "crwHierData"
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    {
      "page": "crwHierSim",
      "title": "Constructor of 'crwHierSim' objects",
      "topics": [
        "crwHierSim"
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    {
      "page": "crwSim",
      "title": "Constructor of 'crwSim' objects",
      "topics": [
        "crwSim"
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    {
      "page": "dbern_rcpp",
      "title": "Bernoulli density function",
      "topics": [
        "dbern_rcpp"
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    },
    {
      "page": "dbeta_rcpp",
      "title": "Probability density function of the beta distribution (written in C++)",
      "topics": [
        "dbeta_rcpp"
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    },
    {
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      "title": "Categorical density function",
      "topics": [
        "dcat_rcpp"
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    },
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      "title": "Exponential density function",
      "topics": [
        "dexp_rcpp"
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    },
    {
      "page": "dgamma_rcpp",
      "title": "Gamma density function",
      "topics": [
        "dgamma_rcpp"
      ]
    },
    {
      "page": "distAngle",
      "title": "Calculate distance between points y and z and turning angle between points x, y, and z",
      "topics": [
        "distAngle"
      ]
    },
    {
      "page": "dlnorm_rcpp",
      "title": "Log-normal density function",
      "topics": [
        "dlnorm_rcpp"
      ]
    },
    {
      "page": "dlogis_rcpp",
      "title": "logistic density function",
      "topics": [
        "dlogis_rcpp"
      ]
    },
    {
      "page": "dmvnorm_rcpp",
      "title": "C++ implementation of multivariate Normal probability density function for multiple inputs",
      "topics": [
        "dmvnorm_rcpp"
      ]
    },
    {
      "page": "dnbinom_rcpp",
      "title": "negative binomial density function",
      "topics": [
        "dnbinom_rcpp"
      ]
    },
    {
      "page": "dnorm_rcpp",
      "title": "Normal density function",
      "topics": [
        "dnorm_rcpp"
      ]
    },
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      "page": "dpois_rcpp",
      "title": "Poisson density function",
      "topics": [
        "dpois_rcpp"
      ]
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      "title": "student t density function",
      "topics": [
        "dt_rcpp"
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      "title": "Von Mises density function",
      "topics": [
        "dvm_rcpp"
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    },
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      "title": "Weibull density function",
      "topics": [
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      "title": "Wrapped Cauchy density function",
      "topics": [
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      "title": "Example dataset",
      "topics": [
        "example",
        "exampleData",
        "forest",
        "miExample"
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    },
    {
      "page": "expandPar",
      "title": "Expand vector of free working parameters to vector of all working parameters including any fixed parameters (used in fitHMM.R and nLogLike.R)",
      "topics": [
        "expandPar"
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    },
    {
      "page": "fitHMM",
      "title": "Fit a multivariate HMM to the data",
      "topics": [
        "fitHMM",
        "fitHMM.momentuHierHMMData",
        "fitHMM.momentuHMMData"
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    {
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      "title": "Convert hierarchical HMM structure to a conventional HMM",
      "topics": [
        "formatHierHMM"
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    },
    {
      "page": "getCovNames",
      "title": "Get names of any covariates used in probability distribution parameters",
      "topics": [
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    },
    {
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      "title": "Get design matrix",
      "topics": [
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    },
    {
      "page": "getPar",
      "title": "Get starting values from momentuHMM, miHMM, or miSum object returned by fitHMM, MIfitHMM, or MIpool",
      "topics": [
        "getPar"
      ]
    },
    {
      "page": "getPar0",
      "title": "Get starting values for new model from existing 'momentuHMM' or 'momentuHierHMM' model fit",
      "topics": [
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        "getPar0.default",
        "getPar0.hierarchical"
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    },
    {
      "page": "getParDM",
      "title": "Get starting values on working scale based on design matrix and other parameter constraints",
      "topics": [
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